Limits...
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.

Halfon MS, Gallo SM, Bergman CM - Nucleic Acids Res. (2007)

Bottom Line: Drosophila melanogaster, with its well-annotated genome, exceptional resources for comparative genomics and long history of experimental studies of transcriptional regulation, represents the ideal system for regulatory bioinformatics.We have merged two existing Drosophila resources, the REDfly database of cis-regulatory modules and the FlyReg database of transcription factor binding sites (TFBSs), into a single integrated database containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites.With the enhanced functionality made possible through this integration of TFBS data into REDfly, together with additional improvements to the REDfly infrastructure, we have constructed a one-stop portal for Drosophila cis-regulatory data that will serve as a powerful resource for both computational and experimental studies of transcriptional regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY 14214, USA. mshalfon@buffalo.edu

ABSTRACT
The identification and study of the cis-regulatory elements that control gene expression are important areas of biological research, but few resources exist to facilitate large-scale bioinformatics studies of cis-regulation in metazoan species. Drosophila melanogaster, with its well-annotated genome, exceptional resources for comparative genomics and long history of experimental studies of transcriptional regulation, represents the ideal system for regulatory bioinformatics. We have merged two existing Drosophila resources, the REDfly database of cis-regulatory modules and the FlyReg database of transcription factor binding sites (TFBSs), into a single integrated database containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites. With the enhanced functionality made possible through this integration of TFBS data into REDfly, together with additional improvements to the REDfly infrastructure, we have constructed a one-stop portal for Drosophila cis-regulatory data that will serve as a powerful resource for both computational and experimental studies of transcriptional regulation. REDfly is freely accessible at http://redfly.ccr.buffalo.edu.

Show MeSH
Integration of CRM and TFBS records. An exciting new feature in REDfly is its cross-referencing of CRMs with any TFBSs that fall within them. Panel A shows the detailed view page for the CRM Dll_208, which contains three footprinted TFBSs with records in REDfly. The arrow indicates the link to the record for one of these three TFBSs, Ubx_Dll:REDFLY:TF000513. Panel B shows the record obtained through the link indicated in panel A. Note that the lookup is functional in both directions; from this TFBS record page, there is a link to the CRM in which the binding site is located (arrow).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238825&req=5

Figure 2: Integration of CRM and TFBS records. An exciting new feature in REDfly is its cross-referencing of CRMs with any TFBSs that fall within them. Panel A shows the detailed view page for the CRM Dll_208, which contains three footprinted TFBSs with records in REDfly. The arrow indicates the link to the record for one of these three TFBSs, Ubx_Dll:REDFLY:TF000513. Panel B shows the record obtained through the link indicated in panel A. Note that the lookup is functional in both directions; from this TFBS record page, there is a link to the CRM in which the binding site is located (arrow).

Mentions: A major advantage of integrating the REDfly and FlyReg databases is the unprecedented level of detailed information that can now be obtained by mapping TFBSs directly to the CRMs of which they are a part. Upon entry of a new CRM or TFBS, the sequence coordinates of the new element are checked against the coordinates of all of the stored TFBSs or CRMs, respectively. If a TFBS falls within a known CRM, the name of the CRM and a link to its REDfly record is provided. Similarly, all CRM records are linked to the REDfly annotations of any TFBSs that fall within them (Figure 2). Searches of REDfly can be restricted to just those TFBSs that map to known CRMs, and vice-versa. Currently, 70% of TFBSs in REDfly map to a known CRM, while 26% of CRMs contain annotated TFBSs. Using these new REDfly features, it is now possible, for example, to investigate the association of TFBS sequences with expression patterns via their corresponding CRMs. REDfly is the only resource for regulatory bioinformatics that provides such a highly integrated annotation of CRMs and their constituent TFBSs.Figure 2.


REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.

Halfon MS, Gallo SM, Bergman CM - Nucleic Acids Res. (2007)

Integration of CRM and TFBS records. An exciting new feature in REDfly is its cross-referencing of CRMs with any TFBSs that fall within them. Panel A shows the detailed view page for the CRM Dll_208, which contains three footprinted TFBSs with records in REDfly. The arrow indicates the link to the record for one of these three TFBSs, Ubx_Dll:REDFLY:TF000513. Panel B shows the record obtained through the link indicated in panel A. Note that the lookup is functional in both directions; from this TFBS record page, there is a link to the CRM in which the binding site is located (arrow).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238825&req=5

Figure 2: Integration of CRM and TFBS records. An exciting new feature in REDfly is its cross-referencing of CRMs with any TFBSs that fall within them. Panel A shows the detailed view page for the CRM Dll_208, which contains three footprinted TFBSs with records in REDfly. The arrow indicates the link to the record for one of these three TFBSs, Ubx_Dll:REDFLY:TF000513. Panel B shows the record obtained through the link indicated in panel A. Note that the lookup is functional in both directions; from this TFBS record page, there is a link to the CRM in which the binding site is located (arrow).
Mentions: A major advantage of integrating the REDfly and FlyReg databases is the unprecedented level of detailed information that can now be obtained by mapping TFBSs directly to the CRMs of which they are a part. Upon entry of a new CRM or TFBS, the sequence coordinates of the new element are checked against the coordinates of all of the stored TFBSs or CRMs, respectively. If a TFBS falls within a known CRM, the name of the CRM and a link to its REDfly record is provided. Similarly, all CRM records are linked to the REDfly annotations of any TFBSs that fall within them (Figure 2). Searches of REDfly can be restricted to just those TFBSs that map to known CRMs, and vice-versa. Currently, 70% of TFBSs in REDfly map to a known CRM, while 26% of CRMs contain annotated TFBSs. Using these new REDfly features, it is now possible, for example, to investigate the association of TFBS sequences with expression patterns via their corresponding CRMs. REDfly is the only resource for regulatory bioinformatics that provides such a highly integrated annotation of CRMs and their constituent TFBSs.Figure 2.

Bottom Line: Drosophila melanogaster, with its well-annotated genome, exceptional resources for comparative genomics and long history of experimental studies of transcriptional regulation, represents the ideal system for regulatory bioinformatics.We have merged two existing Drosophila resources, the REDfly database of cis-regulatory modules and the FlyReg database of transcription factor binding sites (TFBSs), into a single integrated database containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites.With the enhanced functionality made possible through this integration of TFBS data into REDfly, together with additional improvements to the REDfly infrastructure, we have constructed a one-stop portal for Drosophila cis-regulatory data that will serve as a powerful resource for both computational and experimental studies of transcriptional regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY 14214, USA. mshalfon@buffalo.edu

ABSTRACT
The identification and study of the cis-regulatory elements that control gene expression are important areas of biological research, but few resources exist to facilitate large-scale bioinformatics studies of cis-regulation in metazoan species. Drosophila melanogaster, with its well-annotated genome, exceptional resources for comparative genomics and long history of experimental studies of transcriptional regulation, represents the ideal system for regulatory bioinformatics. We have merged two existing Drosophila resources, the REDfly database of cis-regulatory modules and the FlyReg database of transcription factor binding sites (TFBSs), into a single integrated database containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites. With the enhanced functionality made possible through this integration of TFBS data into REDfly, together with additional improvements to the REDfly infrastructure, we have constructed a one-stop portal for Drosophila cis-regulatory data that will serve as a powerful resource for both computational and experimental studies of transcriptional regulation. REDfly is freely accessible at http://redfly.ccr.buffalo.edu.

Show MeSH